1,720,966 research outputs found
Giant sulfur bacteria (Beggiatoaceae) from sediments below the Benguela Upwelling System the host diverse microbiomes
No full textDue to their lithotrophic metabolisms, morphological complexity and conspicuous appearance, members of the Beggiatoaceae have been extensively studied for more than 100 years. These bacteria are known to be primarily sulfur-oxidizing autotrophs that commonly occur in dense mats at redox interfaces. Their large size and the presence of a mucous sheath allows these cells to serve as sites of attachment for communities of other microorganisms. But little is known about their individual niche preferences and attached microbiomes, particularly in marine environments, due to a paucity of cultivars and their prevalence in habitats that are difficult to access and study. Therefore, in this study, we compare Beggiatoaceae strain composition, community composition, and geochemical profiles collected from sulfidic sediments at four marine stations off the coast of Namibia. To elucidate community members that were directly attached and enriched in both filamentous Beggiatoaceae, namely Ca. Marithioploca spp. and Ca. Maribeggiatoa spp., and non-filamentous Beggiatoaceae, Ca. Thiomargarita spp., the two morphotypes were rinsed of sediment debris and pooled by morphotype for iTag sequencing. The Beggiatoaceae samples collected from a highly sulfidic site were enriched in strains of sulfur-oxidizing Campylobacterota, who may promote a more hospitable setting for the Beggiatoaceae who are known to have a lower tolerance for sulfide to oxygen ratios. Otherwise, specific Beggiatoaceae niche preferences were not elucidated by the methods employed in this study. We found just a few host-specific associations with the motile filamentous morphotypes. On the contrary, we detected 123 host specific enrichments with non-motile chain forming Beggiatoaceae. Potential metabolisms of the enriched strains include fermentation of host sheath, syntrophic exchange of H2 and acetate, inorganic sulfur metabolism, and nitrite oxidation. Surprisingly, we did not detect any enrichments of anaerobic ammonium oxidizing bacteria as previously suggested and postulate that less well-studied anaerobic ammonium oxidation pathways may be occurring instead.Simons Foundation award #341838National Science Foundation award #1935351Flood, Beverly E.; Bailey, Jake V.. (2021). Giant sulfur bacteria (Beggiatoaceae) from sediments below the Benguela Upwelling System the host diverse microbiomes. Retrieved from the University Digital Conservancy, https://doi.org/10.13020/9td6-c784
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Fluoride and Gallein Inhibit Polyphosphate Accumulation by Oral Pathogen Rothia dentocariosa - Data Sharing Archive
No full textProtocol Description, Raw Data Results, and Figure Data from collaboration between Earth and Environmental Science and the School of Dentistry.This raw data set supports publication found in Letters in Applied Microbiology:
The uptake and storage of extracellular orthophosphate (Pi) by polyphosphate (polyP) accumulating bacteria may contribute to mineral dissolution in the oral cavity. To test the effect of potential inhibitors of polyP kinases on Rothia dentocariosa, gallein (0, 25, 50, 100 µM) and fluoride (0, 50, 100 ppm) were added to R. dentocariosa cultures grown in brain heart infusion broth. At late log growth phase (8h), extracellular Pi was measured using an ascorbic acid assay, and polyP was isolated from bacterial cells treated with RNA/DNAases using a neutral phenol/chloroform extraction. Extracts were hydrolyzed and quantified as above. Gallein and fluoride had minor effects on bacterial growth with NaF having a direct effect on media pH. Gallein (≥25 µM) and fluoride (≥50 ppm) attenuated the bacterial drawdown of extracellular Pi 56.7% (p <0.05) and 37.3% (p <0.01). There was a corresponding polyP synthesis decrease of 73.2% (p<0.0001) from gallein and 83.1% (p<0.0001) from fluoride. Attenuated total reflectance Fourier transform infrared spectroscopy validated the presence of polyP and its reduced concentration in R. dentocariosa bacterial cells following gallein and fluoride treatment. R. dentocariosa can directly change extracellular Pi and accumulate intracellular polyP but the mechanism is attenuated by gallein and NaF.NIH/NIDCR R01DE027669Kumar, Dhiraj; Mandal, Subhrangshu; Bailey, Jake V.; Flood, Beverly E.; Jones, Robert S. (2023). Fluoride and Gallein Inhibit Polyphosphate Accumulation by Oral Pathogen Rothia dentocariosa - Data Sharing Archive. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/d7wn-7n44
Ex vivo Uptake of Enamel Phosphate by Rothia dentocariosa and Gallein Inhibition - Data Sharing Archive
No full textThis record contains the underlying data for manuscript figures 2A - 5D.A novel demineralization model tested the hypothesis that R. dentocariosa (Rd) can directly ingest tooth-derived orthophosphate (Pi). The study also examined if the internalization of tooth-derived Pi could be attenuated with gallein, an inhibitor of polyphosphate (polyP) kinases. Radionuclide 32P labeled remineralized bovine enamel (n=6) was exposed to Rothia dentocariosa (ATCC 17931) incubated in brain heart infusion (BHI) broth containing glucose. Attenuated total reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy and cross-polarization optical coherence tomography assessed the surface and subsurface characteristics of the remineralized and demineralized enamel surface. Liquid scintillation traced the 32P release from the tooth to the intracellular polyP in galleinpos/neg samples. FTIR determined that 32P was incorporated in dental enamel lesions and was released after exposure to an acidic buffer (pH=4.5) or Rd. After 24 hrs of exposure, galleinpos reduced R. dentocariosa’s planktonic growth and increased pH by 7.45% and 7.19% respectively compared to galleinneg. Planktonic cultures of R. dentocariosa galleinpos (25, 50, 100 mM) after 24 hrs decreased the ability of planktonic bacteria to be cultured directly on BHI agar plates by an order of magnitude more than galleinneg samples. Isotope labeling demonstrated that R. dentocariosa used Pi derived directly from the tooth for the benefit of the bacterium’s fitness through the formation of polyP. Gallein attenuated polyP accumulation, reduced bacterial cultivability, and may be a potential therapy option in the prevention and treatment of primary and secondary caries.This study was funded by NIH grant R01 DE027669.Kumar, Dhiraj; Jones, Robert S.; Flood, Beverly E.; Bailey, Jake V.. (2025). Ex vivo Uptake of Enamel Phosphate by Rothia dentocariosa and Gallein Inhibition - Data Sharing Archive. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://hdl.handle.net/11299/276448
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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